Index – E

E() (in module pyrosetta.rosetta.ObjexxFCL.format) e1() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) e2() (pyrosetta.rosetta.numeric.expression_parser.AndExpression method) (pyrosetta.rosetta.numeric.expression_parser.EqualsExpression method) (pyrosetta.rosetta.numeric.expression_parser.GTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.GT_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LTE_Expression method) (pyrosetta.rosetta.numeric.expression_parser.LT_Expression method) (pyrosetta.rosetta.protocols.pack_daemon.VMaxBy method) (pyrosetta.rosetta.protocols.pack_daemon.VMinBy method) E_elec() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) E_solv() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) E_solv_pair() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) E_solv_self() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) Edge (class in pyrosetta.rosetta.core.kinematics) edge() (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) edge_label() (pyrosetta.rosetta.core.kinematics.FoldTree method) edge_list_begin() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) edge_list_end() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.protocols.hbnet.HBondNode method) (pyrosetta.rosetta.protocols.sewing.ModelNode method) (pyrosetta.rosetta.protocols.sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) edge_list_iterator_at_end() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) EdgeList (class in pyrosetta.rosetta.utility.graph) EdgeListConstIterator (class in pyrosetta.rosetta.utility.graph) EdgeListElement (class in pyrosetta.rosetta.utility.graph) EdgeListIterator (class in pyrosetta.rosetta.utility.graph) effective_lower_terminus_based_on_working_res() (in module pyrosetta.rosetta.core.pose) effective_sequence_separation() (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) effective_upper_terminus_based_on_working_res() (in module pyrosetta.rosetta.core.pose) Efield_fixed() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) Efield_induced() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) Efield_rf_fixed() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) Efield_rf_induced() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) eggshell_coord_list() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) EggshellGrid (class in pyrosetta.rosetta.protocols.pockets) Ei() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) eigenvalue_jacobi() (in module pyrosetta.rosetta.numeric) eigenvector_jacobi() (in module pyrosetta.rosetta.numeric) EItem (class in pyrosetta.rosetta.core.optimization) elapsed_time() (pyrosetta.rosetta.protocols.jd2.Job method) elec_die() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_group_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_max_dis() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_min_dis() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_no_dis_dep_die() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_sigmoidal_die() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elec_sigmoidal_die_params() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) elecF2() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) ElectronConfiguration (class in pyrosetta.rosetta.core.chemical) ElectronDensityLoaderCreator (class in pyrosetta.rosetta.core.scoring.electron_density) ElectronDensityOptionsCreator (class in pyrosetta.rosetta.core.scoring.electron_density) elem_length() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) Element (class in pyrosetta.rosetta.core.chemical) element() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.Element method) (pyrosetta.rosetta.core.chemical.ElementSet method) Element.Properties (class in pyrosetta.rosetta.core.chemical) element2name() (in module pyrosetta.rosetta.core.chemical.element) element_from_string() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) element_index() (pyrosetta.rosetta.core.chemical.ElementSet method) element_list() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) element_name() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) element_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeSet method) element_set_ptr() (pyrosetta.rosetta.core.chemical.ResidueType method) element_summary_as_simple_subelement() (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList method) element_type() (pyrosetta.rosetta.core.chemical.Atom method) element_type_def() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) elements_from_name() (in module pyrosetta.rosetta.core.chemical.element) ElementSet (class in pyrosetta.rosetta.core.chemical) EllipsoidalRandomizationMover (class in pyrosetta.rosetta.protocols.docking) EMapVector (class in pyrosetta.rosetta.core.scoring) EmbeddingDef (class in pyrosetta.rosetta.protocols.membrane.geometry) emergency_rotamer() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) emit_intermediate() (in module pyrosetta.rosetta.protocols.nonlocal) (in module pyrosetta.rosetta.protocols.star) Emitter (class in pyrosetta.rosetta.basic) EMPTY (class in pyrosetta.rosetta.core.pack.task) empty() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.pose.reference_pose.ReferencePoseSet method) (pyrosetta.rosetta.core.scoring.DenseEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) (pyrosetta.rosetta.core.scoring.PolymerBondedEnergyContainer method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.signals.Link method) empty_clone() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) empty_pose() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) empty_record() (pyrosetta.rosetta.core.pose.PDBInfo method) empty_sfxn() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) enable() (pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints method) enable_autotemp() (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) enable_benchmark_mode() (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.ModelCDRH3 method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) enable_build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) enable_centroid_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) enable_constraint_scoreterms() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) enable_custom_variant_types() (pyrosetta.rosetta.core.chemical.ResidueProperties method) (pyrosetta.rosetta.core.chemical.ResidueType method) enable_end_bias_check() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) enable_fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) enable_graft_h1() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_h2() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_h3() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_l1() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_l2() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_graft_l3() (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) enable_ignorefinished() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) enable_inprogress() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) enable_MPI_reroute() (pyrosetta.rosetta.utility.io.ozstream method) enable_output() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) enable_sampling_of_loop_takeoff() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close) enabled() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) EnableMultiCoolAnnealer (class in pyrosetta.rosetta.core.pack.task.operation) enclosing_angles() (in module pyrosetta.rosetta.core.membrane) encode6bit() (in module pyrosetta.rosetta.utility) encode_24_to_32() (in module pyrosetta.rosetta.utility) end() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.anchored_design.Anchor method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.jumping.Interval method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBResidueRange method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) end1() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) end_atomid() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) end_atoms1() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) end_atoms2() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) end_bias() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) end_bias_check() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) end_bias_check_enabled() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) end_bias_probabilities() (in module pyrosetta.rosetta.protocols.medal) end_const() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) end_critical_section() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) end_list() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) end_map() (pyrosetta.rosetta.basic.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.YamlEmitter method) end_of_queue() (pyrosetta.rosetta.utility.recent_history_queue method) end_output_writing() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) end_receptor_partner_pair() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) end_res() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) end_structure() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) end_time() (pyrosetta.rosetta.protocols.jd2.Job method) end_timing() (pyrosetta.rosetta.protocols.jd2.Job method) ending_node() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) endswith() (in module pyrosetta.rosetta.utility) EndToEndPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) Energies (class in pyrosetta.rosetta.core.scoring) energies() (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.pose.Pose method) energies_from_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) energies_into_pose() (pyrosetta.rosetta.core.io.silent.SilentStruct method) energies_matrix() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) energies_not_yet_computed() (pyrosetta.rosetta.core.scoring.EnergyEdge method) energies_updated() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) (pyrosetta.rosetta.protocols.hbnet.HBondEdge method) energy_computed() (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) energy_cutoff() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) energy_from_pose() (in module pyrosetta.rosetta.core.pose) energy_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) energy_matrices() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) energy_matrix() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) energy_method_options() (pyrosetta.rosetta.core.scoring.ScoreFunction method) energy_names() (pyrosetta.rosetta.core.io.silent.SilentStruct method) energy_terms() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) EnergyCutRotamerTrialsMinMover (class in pyrosetta.rosetta.protocols.simple_moves) EnergyEdge (class in pyrosetta.rosetta.core.scoring) EnergyEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) EnergyEvent (class in pyrosetta.rosetta.core.pose.signals) EnergyGraph (class in pyrosetta.rosetta.core.scoring) EnergyLandscapeEvaluator (class in pyrosetta.rosetta.protocols.toolbox) EnergyMethod (class in pyrosetta) (class in pyrosetta.rosetta.core.scoring.methods) EnergyMethodCreator (class in pyrosetta.rosetta.core.scoring.methods) EnergyMethodOptions (class in pyrosetta.rosetta.core.scoring.methods) EnergyNode (class in pyrosetta.rosetta.core.scoring) EnergyReporter (class in pyrosetta.rosetta.protocols.pose_reporters) enforce_all_waters() (in module pyrosetta.rosetta.protocols.hydrate) enforce_minimum_length() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) enlarge_h_lj_wdepth() (in module pyrosetta.rosetta.core.chemical) enough_connections() (pyrosetta.rosetta.protocols.simple_filters.RegionalConnections method) enqueue() (pyrosetta.rosetta.protocols.moves.CyclicMover method) EnsembleJobInputter (class in pyrosetta.rosetta.protocols.jd2) ensure_directory_for_out_silent_file_exists() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) ensure_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.protocols.rna.denovo) ensure_site() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) ensure_size() (pyrosetta.rosetta.core.optimization.Particle method) ensure_valid_full_seq_num() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) Entity (class in pyrosetta.rosetta.protocols.genetic_algorithm) entity_elements_from_1letterstring() (in module pyrosetta.rosetta.protocols.multistate_design) entity_length() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) entity_template() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) EntityElement (class in pyrosetta.rosetta.protocols.genetic_algorithm) EntityElementCreator (class in pyrosetta.rosetta.protocols.genetic_algorithm) EntityElementFactory (class in pyrosetta.rosetta.protocols.genetic_algorithm) EntityRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) Enum (class in pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType) (class in pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType) (class in pyrosetta.rosetta.protocols.forge.build.BuildInstructionState) (class in pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme) (class in pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage) (class in pyrosetta.rosetta.protocols.jd2.JobInputterInputSource) enumerate() (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) enumerate_permutations() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) enumeration_shell() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) envsmooth_zero_negatives() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) enz_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) EnzConstraintParameters (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) enzcst_io() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) EnzCstTemplateRes (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzCstTemplateResAtoms (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzdesCstCache (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzdesJobOutputter (class in pyrosetta.rosetta.protocols.enzdes) EnzdesLoopsFile (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) EnzdesScorefileFilter (class in pyrosetta.rosetta.protocols.enzdes) EnzymaticMover (class in pyrosetta.rosetta.protocols.enzymatic_movers) EnzymeData (class in pyrosetta.rosetta.core.enzymes) EnzymeManager (class in pyrosetta.rosetta.core.enzymes) eof() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) epsilon() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) epsilon_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) epsilon_north() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) epsilon_south() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) epslon() (in module pyrosetta.rosetta.numeric.linear_algebra) equal() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) equal_by_epsilon() (in module pyrosetta.rosetta.numeric) equal_size() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) equali() (in module pyrosetta.rosetta.ObjexxFCL) equals() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) equals_string() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) EqualsExpression (class in pyrosetta.rosetta.numeric.expression_parser) erase() (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.protocols.frags.SingleResidueTorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) erase_comment() (pyrosetta.rosetta.core.io.silent.SilentStruct method) erase_hit() (pyrosetta.rosetta.protocols.match.Matcher method) erfcc() (in module pyrosetta.rosetta.numeric.model_quality) errf() (in module pyrosetta.rosetta.numeric.statistics) errfc() (in module pyrosetta.rosetta.numeric.statistics) errfcx() (in module pyrosetta.rosetta.numeric.statistics) errfi() (in module pyrosetta.rosetta.numeric.statistics) Error() (in module pyrosetta.rosetta.basic) error() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) error_check_requested_adducts() (in module pyrosetta.rosetta.core.chemical) esolvE() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) estimate_dfunc() (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) estimate_membrane_center() (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) estimate_sidechain_depth() (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthCalculator method) Etable (class in pyrosetta.rosetta.core.scoring.etable) etable_atom_pair_energies() (in module pyrosetta) etable_disbins() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) etable_energy() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) etable_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) etable_type() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) EtableEvaluator (class in pyrosetta.rosetta.core.scoring.etable) EtableFunc (class in pyrosetta.rosetta.core.scoring.func) EtableParamsOnePair (class in pyrosetta.rosetta.core.scoring.etable)

euler_offsets() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) eval() (pyrosetta.rosetta.protocols.jumping.SameStrand method) eval_atom_derivative() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.GenBornPotential method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) eval_atom_derivative_base_base() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivative_rna_backbone_backbone() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivative_rna_base_backbone() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivative_rna_repulsive() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_atom_derivatives_for_minedge() (in module pyrosetta.rosetta.core.scoring) eval_atom_derivatives_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_atom_nonpolar_derivative() (pyrosetta.rosetta.core.scoring.FACTSPotential method) eval_atom_polar_derivative() (pyrosetta.rosetta.core.scoring.FACTSPotential method) eval_bbbb_sr2b_energies() (in module pyrosetta.rosetta.core.scoring) eval_bbsc_sr2b_energies() (in module pyrosetta.rosetta.core.scoring) eval_cd_1b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b_bb_bb() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b_bb_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_2b_sc_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cd_intrares_energy() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_1b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b_bb_bb() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b_bb_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_2b_sc_sc() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_ci_intrares_energy() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_cubic_polynomial() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) eval_dE_dR_over_r_v() (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) eval_dof_deriv_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_dof_derivative() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_impl() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) eval_intrares_derivatives() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intrares_elec_ST_only() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) eval_intrares_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intrares_energy_ext() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intraresidue_dof_derivative() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_intrsres_elec_ST_only() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) eval_long_range_twobody_energies() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_lowest_score_pose() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) eval_multibody_atom_derivative() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) eval_non_residue_pair_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintSet method) eval_npd_atom_derivative() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_onebody_energies() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_res() (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_res_onebody_energies_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_res_pair_energy_for_minedge() (in module pyrosetta.rosetta.core.scoring) eval_residue_derivatives() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) eval_residue_dof_derivative() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) eval_residue_pair_derivatives() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.VdWTinkerPotential method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) eval_residue_pair_derivatives_sorted() (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) eval_rna_base_pair_energy() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) eval_rotameric_energy_bb_dof_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) eval_rotameric_energy_deriv() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) eval_scsc_sr2b_energies() (in module pyrosetta.rosetta.core.scoring) eval_twobody_neighbor_energies() (pyrosetta.rosetta.core.scoring.ScoreFunction method) eval_weighted_atom_derivatives_for_minedge() (in module pyrosetta.rosetta.core.scoring) eval_weighted_dof_deriv_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_weighted_res_onebody_energies_for_minnode() (in module pyrosetta.rosetta.core.scoring) eval_weighted_res_pair_energy_for_minedge() (in module pyrosetta.rosetta.core.scoring) evalpoly() (in module pyrosetta.rosetta.numeric.kinematic_closure) evaluate() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) evaluate_cbeta() (pyrosetta.rosetta.core.scoring.MembranePotential method) evaluate_constraints() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) evaluate_contact_score() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) evaluate_derivative() (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunction method) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferencesFunction method) evaluate_env() (pyrosetta.rosetta.core.scoring.MembranePotential method) evaluate_env_and_cbeta_deriv() (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_env_and_cbeta_scores() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_env_score() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) evaluate_local() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) evaluate_nonpolar_energy() (pyrosetta.rosetta.core.scoring.FACTSPotential method) evaluate_pair() (pyrosetta.rosetta.core.scoring.MembranePotential method) evaluate_pair_and_cenpack_deriv() (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_pair_and_cenpack_score() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) evaluate_pair_and_vdw_score() (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) evaluate_polar_energy() (pyrosetta.rosetta.core.scoring.FACTSPotential method) evaluate_polar_otf_energy() (pyrosetta.rosetta.core.scoring.FACTSPotential method) evaluate_pose() (in module pyrosetta.rosetta.protocols.evaluation) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) evaluate_positive_states() (pyrosetta.rosetta.protocols.multistate_design.MultiStatePacker method) evaluate_residues() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) evaluate_rnp_aa_rna_backbone_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) evaluate_rnp_base_pair_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) evaluate_rnp_pair_score() (pyrosetta.rosetta.core.scoring.rna.RNP_LowResPotential method) evaluate_rotamer_background_energies() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_background_energy_maps() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_intrares_energies() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_intrares_energy_maps() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_rotamer_pair_energies() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) evaluate_silent_struct() (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) EvaluatedArchive (class in pyrosetta.rosetta.protocols.jd2.archive) evaluator() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) EvaluatorCreator (class in pyrosetta.rosetta.protocols.evaluation) EvaluatorFactory (class in pyrosetta.rosetta.protocols.evaluation) evaluators() (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) events() (pyrosetta.rosetta.core.pose.datacache.LengthEventCollector method) EX (class in pyrosetta.rosetta.core.pack.task) ex() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) ex1() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro_exposed() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex1aro_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro_exposed() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro_exposed_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex2aro_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex3() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex3_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex4() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ex4_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) EX_CUTOFF (class in pyrosetta.rosetta.core.pack.task) examine_pose() (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) exchange_grid_dim() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) exclude_AA_threshold() (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) exclude_chain_termini() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) exclude_clusters() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_clusters_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_clusters_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_DNA_DNA() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_germlines() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_germlines_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_germlines_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_intra_res_protein() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_monomer_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_pdbs() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_pdbs_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_pdbs_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_protein_protein_fa_elec() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) exclude_site() (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) exclude_species() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_species_add() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_species_clear() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) exclude_variants() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) EXCN_BadInput (class in pyrosetta.rosetta.utility.excn) EXCN_CalcFailed (class in pyrosetta.rosetta.protocols.simple_filters) EXCN_Fold (class in pyrosetta.rosetta.protocols.denovo_design.components) EXCN_Illegal_Arguments (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_InitFailed (class in pyrosetta.rosetta.protocols.simple_filters) EXCN_Membrane (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_Membrane_Bounds (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_MembraneFoldTree (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_NonMembrane (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_Resource_Definition (class in pyrosetta.rosetta.core.conformation.membrane) EXCN_Stop_BFS (class in pyrosetta.rosetta.utility.graph) EXCN_VirtualRsd (class in pyrosetta.rosetta.core.conformation.membrane) exdna_sample_level() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) exec() (pyrosetta.rosetta.core.scoring.APBSWrapper method) execute() (in module pyrosetta.rosetta.basic) ExecutionResult (class in pyrosetta.rosetta.basic) Exemplar (class in pyrosetta.rosetta.protocols.cluster) exit() (in module pyrosetta.rosetta.utility) exit_callback() (pyrosetta.rosetta.utility.py.PyExitCallback method) exit_if_missing_heavy_atoms() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) exp() (pyrosetta.rosetta.ObjexxFCL.Dimension method) exp_clone() (pyrosetta.rosetta.ObjexxFCL.Dimension method) exp_hash() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) exp_p() (pyrosetta.rosetta.ObjexxFCL.Dimension method) expand_loop_takeoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) expand_proton_chis() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) expected_by_properties_absolute() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) expected_by_properties_fraction() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) experimental_technique_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) experimental_technique_to_string() (pyrosetta.rosetta.core.io.HeaderInformation method) experimental_techniques() (pyrosetta.rosetta.core.io.HeaderInformation method) expid() (pyrosetta.rosetta.core.scoring.RDC method) explicit_links_from_sfr_linkage() (in module pyrosetta.rosetta.core.io) explicit_ramp_constraints() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) explicitly_set_movemap() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) exponential_deriv() (in module pyrosetta.rosetta.core.scoring.constraints) export_packer_results() (in module pyrosetta.rosetta.protocols.rna.denovo) Expression (class in pyrosetta.rosetta.numeric.expression_parser) ExpressionCreator (class in pyrosetta.rosetta.numeric.expression_parser) ext() (pyrosetta.rosetta.utility.file.FileName method) extend() (pyrosetta.rosetta.core.fragment.SecondaryStructure method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) extend_CDR() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) extend_sequence_mapping() (in module pyrosetta.rosetta.protocols.loops) extend_to() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) extended_loop() (pyrosetta.rosetta.protocols.LoopRebuild method) ExtendedPoseBuilder (class in pyrosetta.rosetta.protocols.denovo_design.components) extension() (pyrosetta.rosetta.utility.file.FileName method) external_sampler() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) ExternalGeomSampler (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) extra_broker_files() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) extra_chi() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) extra_coord_list() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) extra_data_1() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) extra_data_2() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) extra_data_3() (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) extra_minimize_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) extra_parameter() (pyrosetta.rosetta.core.chemical.AtomType method) extra_parameter_index() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) extra_parameter_indices() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) extra_residues_to_steal() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) extrachi_cutoff() (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) extrachi_sample_level() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) ExtraChiCutoff (class in pyrosetta.rosetta.core.pack.task.operation) extract_asymmetric_unit() (in module pyrosetta.rosetta.core.pose.symmetry) extract_asymmetric_unit_pdb_info() (in module pyrosetta.rosetta.core.pose.symmetry) extract_continuous_chunks() (in module pyrosetta.rosetta.protocols.loops) extract_coordinates_from_pose_1x3() (in module pyrosetta.toolbox.extract_coords_pose) extract_coordinates_from_pose_3x1() (in module pyrosetta.toolbox.extract_coords_pose) extract_fragment() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) extract_int() (in module pyrosetta.rosetta.protocols.denovo_design) extract_rt() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) extract_sasa_for_atom() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) extract_secondary_structure_chunks() (in module pyrosetta.rosetta.protocols.loops) extract_sheets_from_pose() (in module pyrosetta.rosetta.protocols.denovo_design.components) extract_sheets_from_strandlist() (in module pyrosetta.rosetta.protocols.denovo_design.components) extract_tag_from_pose() (in module pyrosetta.rosetta.core.pose) ExtractAsymmetricUnitMover (class in pyrosetta.rosetta.protocols.simple_moves.symmetry) ExtractSmallest() (in module pyrosetta.rosetta.protocols.toolbox) ExtraQuadraticRepulsion (class in pyrosetta.rosetta.core.scoring.etable) ExtraRotamers (class in pyrosetta.rosetta.core.pack.task.operation) ExtraRotamersGeneric (class in pyrosetta.rosetta.core.pack.task.operation) ExtraRotSample (class in pyrosetta.rosetta.core.pack.task) ExtraScoreEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters)